Analyze sequences from iSeq run 5/15/21 and 5/24/21 - Githubissues

hollygene / CornellPostdoc

Various scripts I used during my tenure as a Postdoctoral Associate at Cornell University

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Analyze sequences from iSeq run 5/15/21 and 5/24/21 #13

Open hollygene opened 3 years ago

hollygene commented 3 years ago

Goal: RdRp library

make sure to get wide margins
for diagnostics of sequences

Download sequences from BaseSpace:

unindexed reads > anything interesting?
what assembler for amplicons? > SPAdes
unindexed because robot messed up
equine CoV reference genome
de novo assemble first?
degenerate primers - in hopes of finding new viruses
quasi-species
does isolate mean culture in FIP? > no
serverity of clinical illness in FIP: graded 1-3 also some cats with black-market remdesevir drug - FIP isolates